Update README and JupyterBook (#11)

* Update README

* Update JupyterBook details

Author: WeilerP

README.md

@@ -1,13 +1,16 @@
 # CellRank protocols
 
-This repository provides the protocols and corresponding preprocessing for CellRank-based trajectory inference.
+This repository provides protocols and corresponding preprocessing for CellRank-based trajectory inference.
+Data used in the different use cases is made available in [this](https://doi.org/10.6084/m9.figshare.c.7752290.v1)
+figshare collection.
 
 ## Installation
 
 ```bash
 conda create -n crp-py311 python=3.11 --yes && conda activate crp-py311
-pip install -e .
 
-pip install jupyterlab ipywidgets
+conda install -c conda-forge cellrank
+pip install -e ".[jupyter]"
+
 python -m ipykernel install --user --name crp-py311 --display-name "crp-py311"
 ```

notebooks/_config.yml

@@ -1,9 +1,9 @@
-title: Single-cell analysis repository
+title: CellRank protocol
 author: Philipp Weiler
 execute:
     execute_notebooks: "off"
 
 repository:
-    url: https://github.com/WeilerP/sc_analysis_template
+    url: https://github.com/theislab/cellrank_protocol
 html:
     use_repository_button: true

notebooks/_toc.yml

@@ -3,4 +3,18 @@ root: index
 parts:
     - caption: Template
       chapters:
-          - file: template
+
+    - caption: CytoTRACEKernel
+      chapters:
+          - file: cytrotrace/cellrank
+    - caption: PseudotimeKernel
+      chapters:
+          - file: pseudotime/preprocessing
+          - file: pseudotime/cellrank
+    - caption: RealTimeKernel
+      chapters:
+          - file: realtime/cellrank
+    - caption: VelocityKernel
+      chapters:
+          - file: velocity/preprocessing
+          - file: velocity/cellrank

notebooks/index.md

@@ -1,42 +1,13 @@
-# Single-cell analysis template repository
+# CellRank protocols
 
-This repository acts as a template notebook for the analysis of single-cell data and methods; the corresponding Jupyter
-Book is rendered [here](https://weilerp.github.io/sc_analysis_template/).
-You can check the [CellRank 2 reproducibility repository](https://github.com/theislab/cellrank2_reproducibility)
-for an example repository following the same outline as this template.
-
-## Set up
-
-1. Rename `src/fancypackage/`.
-2. Update `pyproject.toml` to include the correct information
-    - Project name
-    - Project description
-    - Project-specific Python requirements
-    - Project author
-    - Project maintainers
-    - Project URLs
-3. Update `src/fancypackage/core/_constants.py` to include any paths relevant to your analysis and that should be accessible from any script or Jupyter notebook
-4. Update this README to include the relevant information about your project.
-5. Ensure repository settings are set up correctly to build Jupyter Book:
-    - In `Settings > Actions > General > Workflow permissions`: Allow read and write permissions.
-    - In `Settings > Pages > Build and deployment`: Set the branch to `gh-pages`.
+This repository provides the protocols and corresponding preprocessing for CellRank-based trajectory inference.
 
 ## Installation
 
 ```bash
-conda create -n fancyname-pyXX python=X.X --yes && conda activate fancyname-pyXX
-pip install -e ".[dev]"
-pre-commit install
+conda create -n crp-py311 python=3.11 --yes && conda activate crp-py311
+pip install -e .
 
 pip install jupyterlab ipywidgets
-python -m ipykernel install --user --name fancyname-pyXX --display-name "fancyname-pyXX"
+python -m ipykernel install --user --name crp-py311 --display-name "crp-py311"
 ```
-
-## Things to keep in mind
-
-Whenever you use a new single-cell tool, add it to `known_bio` in `pyproject.toml` s.t. `isort` can work correctly.
-
-## Workflow
-
-The workflow for committing a notebook is as follows: Upon committing a notebook, the pre-commit hooks format your notebook
-and generate a corresponding script. You need to add the formatted notebook and Python script to the same commit for the commit to go through. The commit will now either be successful or not. If not, your Python script was formatted by the pre-commit hooks. In that case, you need to update your notebook accordingly, unstage the Python script, and recommit the notebook. You will iterate through this process until there are no inconsistencies between the notebook and its corresponding Python script.